Strain identifier

BacDive ID: 4175

Type strain: Yes

Species: Halodesulfovibrio oceani

Strain Designation: I.8.1

Strain history: K. Finster I.8.1.

NCBI tax ID(s): 983975 (species)

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General

@ref: 15669

BacDive-ID: 4175

DSM-Number: 21390

keywords: 16S sequence, Bacteria, anaerobe, psychrophilic, vibrio-shaped

description: Halodesulfovibrio oceani I.8.1 is an anaerobe, psychrophilic, vibrio-shaped bacterium that was isolated from sea water at 400 m depth, oxygen minimum zone.

NCBI tax id

  • NCBI tax id: 983975
  • Matching level: species

strain history

@refhistory
15669<- K. Finster, Århus Univ., Denmark; I.8.1 <- K. Finster {2007}
67770K. Finster I.8.1.

doi: 10.13145/bacdive4175.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfovibrionales
  • family: Desulfovibrionaceae
  • genus: Halodesulfovibrio
  • species: Halodesulfovibrio oceani
  • full scientific name: Halodesulfovibrio oceani (Finster and Kjeldsen 2012) Shivani et al. 2017

  • synonyms

    • @ref: 20215
    • synonym: Desulfovibrio oceani

@ref: 15669

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfovibrionales

family: Desulfovibrionaceae

genus: Halodesulfovibrio

species: Halodesulfovibrio oceani subsp. oceani

full scientific name: Halodesulfovibrio oceani subsp. oceani (Finster and Kjeldsen 2012) Shivani et al. 2017

strain designation: I.8.1

type strain: yes

Morphology

cell morphology

  • @ref: 25150
  • cell length: 1.0-1.5 µm
  • cell width: 0.3 µm
  • cell shape: vibrio-shaped

Culture and growth conditions

culture medium

  • @ref: 15669
  • name: MARINE DESULFOVIBRIO COMPLEX MEDIUM (DSMZ Medium 1040)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1040
  • composition: Name: MARIDESULFOVIBRIO MEDIUM (DSMZ Medium 1040) Composition: Sea Salt 34.9301 g/l Na-DL-lactate 2.49501 g/l Yeast extract 0.998004 g/l Na2CO3 0.998004 g/l Na2S x 9 H2O 0.299401 g/l MgSO4 x 7 H2O 0.0299401 g/l NaCl 0.00998004 g/l MnSO4 x H2O 0.00499002 g/l (NH4)2Ni(SO4)2 x 6 H2O 0.00279441 g/l CoCl2 x 6 H2O 0.00179641 g/l ZnSO4 x 7 H2O 0.00179641 g/l CaCl2 x 2 H2O 0.000998004 g/l FeSO4 x 7 H2O 0.000998004 g/l Sodium resazurin 0.000499002 g/l AlK(SO4)2 x 12 H2O 0.000179641 g/l CuSO4 x 5 H2O 9.98004e-05 g/l H3BO3 9.98004e-05 g/l Na2MoO4 x 2 H2O 9.98004e-05 g/l Na2WO4 x 2 H2O 9.98004e-05 g/l Na2SeO4 9.98004e-05 g/l Pyridoxine hydrochloride 9.98004e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Folic acid 1.99601e-05 g/l Biotin 1.99601e-05 g/l Vitamin B12 9.98004e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15669positivegrowth20psychrophilic
25150positiveoptimum20psychrophilic
25150positivegrowth4.0-30.0
67770positivegrowth20psychrophilic

culture pH

@refabilitytypepHPH range
25150positiveoptimum7.0-8.0
25150positivegrowth6.0-8.5alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
15669anaerobe
25150obligate anaerobe

halophily

@refsalttested relationconcentrationgrowth
25150NaCloptimum2.5-3.5 %(w/v)
25150NaClgrowth0.1-4.0 %(w/v)positive

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2515030089acetate-electron donor
2515035391aspartate-electron donor
251505291gelatin-hydrolysis
2515027897tryptophan-energy source
2515016150benzoate+electron donor
2515015356cysteine+electron donor
2515017754glycerol+electron donor
2515017822serine+electron donor
2515017359sulfite+electron acceptor

metabolite production

  • @ref: 25150
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 25150
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
25150catalase+1.11.1.6
25150tryptophan deaminase-4.1.99.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
15669sea water at 400 m depth, oxygen minimum zoneoff coastPeruPERMiddle and South America-13.8753-76.7731
67770Oxygen minimum zone water column off the Peru at water depths of 400 and 500 m

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_22671.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15981;96_2533;97_3094;98_3886;99_22671&stattab=map
  • Last taxonomy: Halodesulfovibrio
  • 16S sequence: FJ655907
  • Sequence Identity:
  • Total samples: 5236
  • soil counts: 122
  • aquatic counts: 4673
  • animal counts: 387
  • plant counts: 54

Safety information

risk assessment

  • @ref: 15669
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15669
  • description: Desulfovibrio oceani subsp. oceani strain I.8.1 16S ribosomal RNA gene, partial sequence
  • accession: FJ655907
  • length: 1408
  • database: ena
  • NCBI tax ID: 613183

GC content

@refGC-contentmethod
1566945.1
2515045.1-45.9high performance liquid chromatography (HPLC)
6777045.1high performance liquid chromatography (HPLC)

External links

@ref: 15669

culture collection no.: DSM 21390, JCM 15970

straininfo link

  • @ref: 73675
  • straininfo: 406211

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15669Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21390)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21390
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
25150Y. S. Shivani, Y.,Sasikala, C.,Ramana, C. V.10.1099/ijsem.0.001574Halodesulfovibrio spirochaetisodalis gen. nov. sp. nov. and reclassification of four Desulfovibrio sppIJSEM 67: 87-93 201727902290
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
73675Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406211.1StrainInfo: A central database for resolving microbial strain identifiers